A molecularly imprinted polymer with a specific selectivity for patulin was successfully synthesized. The molecularly imprinted material was prepared using the two functional monomers dopamine and melamine and formaldehyde as the cross-linker. The resulting material possessed a large number of hydrophilic groups, such as hydroxyls, imino groups, and ether linkages. For the first time, uric acid was used as a dummy template for its structural similarity to patulin. Comprehensive characterization and detailed studies of the adsorption process were carried out via adsorption isotherms, while the rate-limiting steps were investigated using adsorption kinetics. Separation, determination, and quantification of patulin were achieved by ultra-high performance liquid chromatography coupled with both photodiode array detection and tandem mass spectrometry. The latter was applied to patulin confirmation in the analysis of real samples. The methodology was validated in 20 apple juice samples. The results showed that the developed hydrophilic molecularly imprinted polymer had high selectivity and specific adsorption towards patulin, with mean recoveries ranging between 85 and 90% and a relative standard deviation lower than 15%. The developed molecularly imprinted polymer exhibited good linearity in the range 1–100 ng mL−1 with coefficient of determination (R2) > 0.99. The limit of detection was 0.5 ng mL−1, and the limit of quantification was 1 ng g−1. The developed method showed a good purification capacity for apple juices due to its hydrophilic nature and the polar interactions established with the target analyte.
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